Correlation between copy number variations of arm-level result and molecular subtypes
Adrenocortical Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1D50K84
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1D50K84
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 68 arm-level results and 8 molecular subtypes across 77 patients, 50 significant findings detected with Q value < 0.25.

  • 4p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 4q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7p gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 7q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 10p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 10q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 12p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12q gain cnv correlated to 'CN_CNMF'.

  • 14q gain cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 16p gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16q gain cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 19q gain cnv correlated to 'CN_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • Xq gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 9p loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 17p loss cnv correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 68 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 50 significant findings detected.

Molecular
subtypes 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
4p gain 0 (0%) 50 6.88e-06
(0.0035) 		0.022
(1.00) 		4.18e-06
(0.00215) 		5.16e-06
(0.00264) 		0.388
(1.00) 		0.47
(1.00) 		0.774
(1.00) 		0.62
(1.00)
4q gain 0 (0%) 52 2.02e-05
(0.0101) 		0.0473
(1.00) 		3.01e-05
(0.0149) 		8.09e-06
(0.0041) 		0.775
(1.00) 		0.856
(1.00) 		1
(1.00) 		0.85
(1.00)
5p gain 0 (0%) 30 2.08e-06
(0.00107) 		0.00469
(1.00) 		1.87e-06
(0.000964) 		2.4e-06
(0.00124) 		1
(1.00) 		0.796
(1.00) 		1
(1.00) 		0.666
(1.00)
5q gain 0 (0%) 32 3.07e-05
(0.0151) 		0.00202
(0.924) 		1.16e-05
(0.00583) 		7.13e-07
(0.000371) 		0.374
(1.00) 		0.928
(1.00) 		0.374
(1.00) 		0.381
(1.00)
7q gain 0 (0%) 40 8.43e-06
(0.00426) 		0.00805
(1.00) 		1.63e-08
(8.53e-06) 		4.72e-06
(0.00241) 		1
(1.00) 		0.861
(1.00) 		1
(1.00) 		0.725
(1.00)
9p gain 0 (0%) 65 7.38e-06
(0.00375) 		0.00205
(0.936) 		0.00037
(0.178) 		0.000143
(0.0693) 		0.204
(1.00) 		0.183
(1.00) 		0.204
(1.00) 		0.221
(1.00)
10p gain 0 (0%) 57 3.26e-05
(0.016) 		0.0356
(1.00) 		3.15e-05
(0.0155) 		0.00018
(0.0871) 		1
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.886
(1.00)
12p gain 0 (0%) 25 3.46e-07
(0.000181) 		0.0653
(1.00) 		1.31e-05
(0.00655) 		0.000423
(0.202) 		0.355
(1.00) 		0.601
(1.00) 		0.355
(1.00) 		0.373
(1.00)
16p gain 0 (0%) 38 2.06e-11
(1.08e-08) 		0.00389
(1.00) 		2.66e-05
(0.0132) 		3.13e-07
(0.000164) 		0.561
(1.00) 		0.435
(1.00) 		1
(1.00) 		0.358
(1.00)
16q gain 0 (0%) 39 5.11e-11
(2.68e-08) 		0.00282
(1.00) 		5.78e-05
(0.0283) 		1.67e-06
(0.000866) 		0.561
(1.00) 		0.435
(1.00) 		1
(1.00) 		0.358
(1.00)
7p gain 0 (0%) 39 0.000577
(0.274) 		0.0269
(1.00) 		1.11e-05
(0.00559) 		0.000373
(0.179) 		0.774
(1.00) 		0.928
(1.00) 		0.774
(1.00) 		1
(1.00)
9q gain 0 (0%) 61 1.13e-05
(0.00566) 		0.00585
(1.00) 		0.00054
(0.257) 		4.17e-05
(0.0205) 		0.436
(1.00) 		0.564
(1.00) 		0.436
(1.00) 		0.747
(1.00)
14q gain 0 (0%) 61 0.00167
(0.764) 		0.0895
(1.00) 		6.6e-05
(0.0323) 		9.01e-05
(0.0438) 		0.00109
(0.514) 		0.00155
(0.713) 		0.00109
(0.514) 		0.00282
(1.00)
19p gain 0 (0%) 35 8.31e-05
(0.0405) 		0.0412
(1.00) 		0.00304
(1.00) 		0.000204
(0.0987) 		0.774
(1.00) 		0.738
(1.00) 		0.774
(1.00) 		0.62
(1.00)
20p gain 0 (0%) 39 2.87e-06
(0.00148) 		0.14
(1.00) 		2.57e-05
(0.0128) 		0.00251
(1.00) 		0.00887
(1.00) 		0.0103
(1.00) 		0.0428
(1.00) 		0.0125
(1.00)
20q gain 0 (0%) 36 1.7e-06
(0.000881) 		0.0354
(1.00) 		1.94e-05
(0.00968) 		0.000838
(0.396) 		0.0798
(1.00) 		0.0876
(1.00) 		0.0798
(1.00) 		0.035
(1.00)
Xq gain 0 (0%) 56 0.000212
(0.102) 		0.136
(1.00) 		5.7e-07
(0.000297) 		0.00513
(1.00) 		1
(1.00) 		0.839
(1.00) 		0.528
(1.00) 		1
(1.00)
9p loss 0 (0%) 66 0.00143
(0.667) 		0.0229
(1.00) 		6.94e-05
(0.0339) 		7.88e-06
(0.004) 		0.0265
(1.00) 		0.183
(1.00) 		0.0265
(1.00) 		0.0563
(1.00)
10q gain 0 (0%) 58 0.0011
(0.514) 		0.0907
(1.00) 		0.000405
(0.194) 		0.00165
(0.757) 		0.486
(1.00) 		0.437
(1.00) 		0.486
(1.00) 		0.787
(1.00)
12q gain 0 (0%) 24 5.92e-06
(0.00302) 		0.355
(1.00) 		0.00146
(0.676) 		0.011
(1.00) 		1
(1.00) 		0.436
(1.00) 		1
(1.00) 		0.383
(1.00)
19q gain 0 (0%) 37 2.32e-05
(0.0115) 		0.0134
(1.00) 		0.00297
(1.00) 		0.000576
(0.274) 		0.385
(1.00) 		0.507
(1.00) 		0.385
(1.00) 		0.387
(1.00)
17p loss 0 (0%) 59 0.00302
(1.00) 		0.000815
(0.385) 		0.000211
(0.102) 		0.00144
(0.669) 		0.711
(1.00) 		0.257
(1.00) 		0.711
(1.00) 		0.473
(1.00)
1q gain 0 (0%) 72 0.306
(1.00) 		0.258
(1.00) 		0.339
(1.00) 		0.057
(1.00) 		1
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.631
(1.00)
2p gain 0 (0%) 71 0.0175
(1.00) 		0.0952
(1.00) 		0.24
(1.00) 		0.0181
(1.00) 		0.579
(1.00) 		0.291
(1.00) 		0.579
(1.00) 		0.278
(1.00)
2q gain 0 (0%) 72 0.306
(1.00) 		0.0371
(1.00) 		0.185
(1.00) 		0.057
(1.00) 		1
(1.00) 		1
(1.00)
3p gain 0 (0%) 69 0.201
(1.00) 		0.303
(1.00) 		0.386
(1.00) 		0.521
(1.00) 		0.386
(1.00) 		0.447
(1.00) 		0.386
(1.00) 		0.521
(1.00)
3q gain 0 (0%) 67 0.305
(1.00) 		0.361
(1.00) 		0.0771
(1.00) 		0.911
(1.00) 		1
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.877
(1.00)
6p gain 0 (0%) 66 0.105
(1.00) 		0.943
(1.00) 		0.18
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
6q gain 0 (0%) 66 0.121
(1.00) 		0.545
(1.00) 		0.368
(1.00) 		0.385
(1.00) 		0.436
(1.00) 		0.564
(1.00) 		0.436
(1.00) 		0.747
(1.00)
8p gain 0 (0%) 50 0.00376
(1.00) 		0.156
(1.00) 		0.0822
(1.00) 		0.111
(1.00) 		0.355
(1.00) 		0.331
(1.00) 		0.758
(1.00) 		0.541
(1.00)
8q gain 0 (0%) 46 0.00836
(1.00) 		0.395
(1.00) 		0.225
(1.00) 		0.292
(1.00) 		0.763
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.845
(1.00)
11q gain 0 (0%) 74 0.304
(1.00) 		0.367
(1.00) 		0.15
(1.00) 		0.47
(1.00) 		1
(1.00) 		1
(1.00)
13q gain 0 (0%) 72 0.726
(1.00) 		0.231
(1.00) 		0.00364
(1.00) 		0.317
(1.00) 		0.617
(1.00) 		0.799
(1.00) 		0.617
(1.00) 		0.812
(1.00)
15q gain 0 (0%) 68 0.00684
(1.00) 		0.0333
(1.00) 		0.0042
(1.00) 		0.00144
(0.667) 		0.112
(1.00) 		0.564
(1.00) 		0.112
(1.00) 		0.282
(1.00)
21q gain 0 (0%) 55 0.00117
(0.547) 		0.0184
(1.00) 		0.0104
(1.00) 		0.00095
(0.447) 		0.355
(1.00) 		0.325
(1.00) 		0.121
(1.00) 		0.248
(1.00)
1p loss 0 (0%) 58 0.0288
(1.00) 		0.0931
(1.00) 		0.14
(1.00) 		0.0534
(1.00) 		0.326
(1.00) 		0.15
(1.00) 		0.326
(1.00) 		0.285
(1.00)
1q loss 0 (0%) 65 0.199
(1.00) 		0.199
(1.00) 		0.873
(1.00) 		0.67
(1.00) 		0.217
(1.00) 		0.269
(1.00) 		0.217
(1.00) 		0.139
(1.00)
2p loss 0 (0%) 68 0.0543
(1.00) 		0.042
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.386
(1.00) 		0.223
(1.00) 		0.386
(1.00) 		0.0969
(1.00)
2q loss 0 (0%) 70 0.00633
(1.00) 		0.00356
(1.00) 		0.454
(1.00) 		0.623
(1.00) 		0.158
(1.00) 		0.0824
(1.00) 		0.158
(1.00) 		0.042
(1.00)
3p loss 0 (0%) 64 0.366
(1.00) 		0.0662
(1.00) 		0.0858
(1.00) 		0.0678
(1.00) 		1
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.404
(1.00)
3q loss 0 (0%) 63 0.0294
(1.00) 		0.0264
(1.00) 		0.0558
(1.00) 		0.00425
(1.00) 		0.678
(1.00) 		0.524
(1.00) 		0.678
(1.00) 		0.712
(1.00)
4p loss 0 (0%) 70 0.0326
(1.00) 		0.028
(1.00) 		0.00133
(0.617) 		0.00398
(1.00) 		1
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.631
(1.00)
4q loss 0 (0%) 68 0.0057
(1.00) 		0.0253
(1.00) 		0.00156
(0.718) 		0.00357
(1.00) 		1
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.631
(1.00)
5p loss 0 (0%) 70 0.772
(1.00) 		0.0883
(1.00) 		0.113
(1.00) 		0.0025
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
5q loss 0 (0%) 71 0.833
(1.00) 		0.0968
(1.00) 		0.017
(1.00) 		0.00906
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
6p loss 0 (0%) 71 0.211
(1.00) 		0.182
(1.00) 		0.755
(1.00) 		0.649
(1.00) 		0.447
(1.00) 		0.447
(1.00)
6q loss 0 (0%) 71 0.211
(1.00) 		0.533
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.194
(1.00) 		0.194
(1.00)
7q loss 0 (0%) 74 0.304
(1.00) 		0.0367
(1.00) 		0.15
(1.00) 		0.0441
(1.00) 		1
(1.00) 		1
(1.00)
8p loss 0 (0%) 68 0.26
(1.00) 		0.382
(1.00) 		0.15
(1.00) 		0.131
(1.00) 		1
(1.00) 		0.373
(1.00) 		1
(1.00) 		0.44
(1.00)
8q loss 0 (0%) 71 0.274
(1.00) 		0.081
(1.00) 		0.0311
(1.00) 		0.0251
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
9q loss 0 (0%) 73 0.561
(1.00) 		0.193
(1.00) 		0.248
(1.00) 		0.0924
(1.00) 		0.117
(1.00) 		0.531
(1.00) 		0.117
(1.00) 		0.273
(1.00)
10p loss 0 (0%) 69 0.178
(1.00) 		0.245
(1.00) 		0.335
(1.00) 		0.311
(1.00) 		0.117
(1.00) 		0.164
(1.00) 		0.117
(1.00) 		0.273
(1.00)
10q loss 0 (0%) 71 0.52
(1.00) 		0.334
(1.00) 		0.574
(1.00) 		0.416
(1.00) 		0.495
(1.00) 		0.495
(1.00)
11p loss 0 (0%) 62 0.00906
(1.00) 		0.0546
(1.00) 		0.22
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.186
(1.00)
11q loss 0 (0%) 64 0.00668
(1.00) 		0.0289
(1.00) 		0.179
(1.00) 		0.686
(1.00) 		1
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.186
(1.00)
12p loss 0 (0%) 74 0.304
(1.00) 		0.0917
(1.00) 		1
(1.00) 		0.259
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
13q loss 0 (0%) 54 0.00384
(1.00) 		0.0692
(1.00) 		0.191
(1.00) 		0.304
(1.00) 		0.342
(1.00) 		0.77
(1.00) 		0.342
(1.00) 		0.628
(1.00)
14q loss 0 (0%) 68 0.00284
(1.00) 		0.0195
(1.00) 		0.0911
(1.00) 		0.0861
(1.00) 		0.311
(1.00) 		0.312
(1.00) 		0.311
(1.00) 		0.202
(1.00)
15q loss 0 (0%) 66 0.295
(1.00) 		0.0351
(1.00) 		0.0333
(1.00) 		0.0435
(1.00) 		0.311
(1.00) 		0.312
(1.00) 		0.311
(1.00) 		0.202
(1.00)
16p loss 0 (0%) 73 0.108
(1.00) 		0.133
(1.00) 		0.0418
(1.00) 		0.211
(1.00) 		0.447
(1.00) 		0.447
(1.00)
16q loss 0 (0%) 73 0.108
(1.00) 		0.00786
(1.00) 		0.0418
(1.00) 		0.0116
(1.00)
17q loss 0 (0%) 63 0.0294
(1.00) 		0.0358
(1.00) 		0.0105
(1.00) 		0.00425
(1.00) 		0.112
(1.00) 		0.166
(1.00) 		0.112
(1.00) 		0.282
(1.00)
18p loss 0 (0%) 53 0.115
(1.00) 		0.042
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.687
(1.00) 		0.52
(1.00) 		0.338
(1.00)
18q loss 0 (0%) 54 0.0603
(1.00) 		0.262
(1.00) 		0.292
(1.00) 		0.858
(1.00) 		0.0999
(1.00) 		0.272
(1.00) 		0.0999
(1.00) 		0.153
(1.00)
20p loss 0 (0%) 72 0.0485
(1.00) 		0.262
(1.00) 		0.0937
(1.00) 		0.0204
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
21q loss 0 (0%) 67 0.0328
(1.00) 		0.202
(1.00) 		0.29
(1.00) 		0.468
(1.00) 		0.644
(1.00) 		0.688
(1.00) 		0.158
(1.00) 		0.135
(1.00)
22q loss 0 (0%) 48 0.106
(1.00) 		0.0096
(1.00) 		0.348
(1.00) 		0.262
(1.00) 		0.197
(1.00) 		0.479
(1.00) 		0.197
(1.00) 		0.244
(1.00)
Xq loss 0 (0%) 69 0.0242
(1.00) 		0.154
(1.00) 		0.587
(1.00) 		0.413
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
'4p gain' versus 'CN_CNMF'

P value = 6.88e-06 (Fisher's exact test), Q value = 0.0035

Table S1.  Gene #6: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
4P GAIN CNV 1 8 12 6
4P GAIN WILD-TYPE 28 11 7 4

Figure S1.  Get High-res Image Gene #6: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 4.18e-06 (Fisher's exact test), Q value = 0.0021

Table S2.  Gene #6: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
4P GAIN CNV 0 7 11 8
4P GAIN WILD-TYPE 24 5 6 15

Figure S2.  Get High-res Image Gene #6: '4p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.16e-06 (Fisher's exact test), Q value = 0.0026

Table S3.  Gene #6: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
4P GAIN CNV 0 13 13
4P GAIN WILD-TYPE 23 19 8

Figure S3.  Get High-res Image Gene #6: '4p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.01

Table S4.  Gene #7: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
4Q GAIN CNV 1 7 12 5
4Q GAIN WILD-TYPE 28 12 7 5

Figure S4.  Get High-res Image Gene #7: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 3.01e-05 (Fisher's exact test), Q value = 0.015

Table S5.  Gene #7: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
4Q GAIN CNV 0 7 9 8
4Q GAIN WILD-TYPE 24 5 8 15

Figure S5.  Get High-res Image Gene #7: '4q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.09e-06 (Fisher's exact test), Q value = 0.0041

Table S6.  Gene #7: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
4Q GAIN CNV 0 11 13
4Q GAIN WILD-TYPE 23 21 8

Figure S6.  Get High-res Image Gene #7: '4q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.0011

Table S7.  Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
5P GAIN CNV 7 17 16 7
5P GAIN WILD-TYPE 22 2 3 3

Figure S7.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1.87e-06 (Fisher's exact test), Q value = 0.00096

Table S8.  Gene #8: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
5P GAIN CNV 4 9 14 19
5P GAIN WILD-TYPE 20 3 3 4

Figure S8.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0012

Table S9.  Gene #8: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
5P GAIN CNV 4 26 16
5P GAIN WILD-TYPE 19 6 5

Figure S9.  Get High-res Image Gene #8: '5p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 3.07e-05 (Fisher's exact test), Q value = 0.015

Table S10.  Gene #9: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
5Q GAIN CNV 7 16 14 8
5Q GAIN WILD-TYPE 22 3 5 2

Figure S10.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 1.16e-05 (Fisher's exact test), Q value = 0.0058

Table S11.  Gene #9: '5q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
5Q GAIN CNV 4 9 14 17
5Q GAIN WILD-TYPE 20 3 3 6

Figure S11.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.13e-07 (Fisher's exact test), Q value = 0.00037

Table S12.  Gene #9: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
5Q GAIN CNV 3 24 17
5Q GAIN WILD-TYPE 20 8 4

Figure S12.  Get High-res Image Gene #9: '5q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0056

Table S13.  Gene #12: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
7P GAIN CNV 4 11 13 10
7P GAIN WILD-TYPE 20 1 4 13

Figure S13.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000373 (Fisher's exact test), Q value = 0.18

Table S14.  Gene #12: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
7P GAIN CNV 5 16 17
7P GAIN WILD-TYPE 18 16 4

Figure S14.  Get High-res Image Gene #12: '7p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 8.43e-06 (Fisher's exact test), Q value = 0.0043

Table S15.  Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
7Q GAIN CNV 4 13 15 5
7Q GAIN WILD-TYPE 25 6 4 5

Figure S15.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1.63e-08 (Fisher's exact test), Q value = 8.5e-06

Table S16.  Gene #13: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
7Q GAIN CNV 2 12 13 10
7Q GAIN WILD-TYPE 22 0 4 13

Figure S16.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.72e-06 (Fisher's exact test), Q value = 0.0024

Table S17.  Gene #13: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
7Q GAIN CNV 3 16 18
7Q GAIN WILD-TYPE 20 16 3

Figure S17.  Get High-res Image Gene #13: '7q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 7.38e-06 (Fisher's exact test), Q value = 0.0037

Table S18.  Gene #16: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
9P GAIN CNV 0 1 10 1
9P GAIN WILD-TYPE 29 18 9 9

Figure S18.  Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.18

Table S19.  Gene #16: '9p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
9P GAIN CNV 0 5 5 1
9P GAIN WILD-TYPE 24 7 12 22

Figure S19.  Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.069

Table S20.  Gene #16: '9p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
9P GAIN CNV 1 1 9
9P GAIN WILD-TYPE 22 31 12

Figure S20.  Get High-res Image Gene #16: '9p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0057

Table S21.  Gene #17: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
9Q GAIN CNV 2 1 12 1
9Q GAIN WILD-TYPE 27 18 7 9

Figure S21.  Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.02

Table S22.  Gene #17: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
9Q GAIN CNV 3 1 11
9Q GAIN WILD-TYPE 20 31 10

Figure S22.  Get High-res Image Gene #17: '9q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 3.26e-05 (Fisher's exact test), Q value = 0.016

Table S23.  Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
10P GAIN CNV 5 1 13 1
10P GAIN WILD-TYPE 24 18 6 9

Figure S23.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 3.15e-05 (Fisher's exact test), Q value = 0.016

Table S24.  Gene #18: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
10P GAIN CNV 4 10 4 2
10P GAIN WILD-TYPE 20 2 13 21

Figure S24.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.087

Table S25.  Gene #18: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
10P GAIN CNV 6 2 12
10P GAIN WILD-TYPE 17 30 9

Figure S25.  Get High-res Image Gene #18: '10p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.000405 (Fisher's exact test), Q value = 0.19

Table S26.  Gene #19: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
10Q GAIN CNV 5 9 3 2
10Q GAIN WILD-TYPE 19 3 14 21

Figure S26.  Get High-res Image Gene #19: '10q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 3.46e-07 (Fisher's exact test), Q value = 0.00018

Table S27.  Gene #21: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
12P GAIN CNV 9 19 16 8
12P GAIN WILD-TYPE 20 0 3 2

Figure S27.  Get High-res Image Gene #21: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1.31e-05 (Fisher's exact test), Q value = 0.0066

Table S28.  Gene #21: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
12P GAIN CNV 7 12 14 18
12P GAIN WILD-TYPE 17 0 3 5

Figure S28.  Get High-res Image Gene #21: '12p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000423 (Fisher's exact test), Q value = 0.2

Table S29.  Gene #21: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
12P GAIN CNV 8 25 18
12P GAIN WILD-TYPE 15 7 3

Figure S29.  Get High-res Image Gene #21: '12p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 5.92e-06 (Fisher's exact test), Q value = 0.003

Table S30.  Gene #22: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
12Q GAIN CNV 10 18 17 8
12Q GAIN WILD-TYPE 19 1 2 2

Figure S30.  Get High-res Image Gene #22: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 6.6e-05 (Fisher's exact test), Q value = 0.032

Table S31.  Gene #24: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
14Q GAIN CNV 2 5 8 0
14Q GAIN WILD-TYPE 22 7 9 23

Figure S31.  Get High-res Image Gene #24: '14q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9.01e-05 (Fisher's exact test), Q value = 0.044

Table S32.  Gene #24: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
14Q GAIN CNV 2 2 11
14Q GAIN WILD-TYPE 21 30 10

Figure S32.  Get High-res Image Gene #24: '14q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 2.06e-11 (Fisher's exact test), Q value = 1.1e-08

Table S33.  Gene #26: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
16P GAIN CNV 3 19 14 3
16P GAIN WILD-TYPE 26 0 5 7

Figure S33.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.013

Table S34.  Gene #26: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
16P GAIN CNV 3 9 13 14
16P GAIN WILD-TYPE 21 3 4 9

Figure S34.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.13e-07 (Fisher's exact test), Q value = 0.00016

Table S35.  Gene #26: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
16P GAIN CNV 2 19 18
16P GAIN WILD-TYPE 21 13 3

Figure S35.  Get High-res Image Gene #26: '16p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 5.11e-11 (Fisher's exact test), Q value = 2.7e-08

Table S36.  Gene #27: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
16Q GAIN CNV 3 19 13 3
16Q GAIN WILD-TYPE 26 0 6 7

Figure S36.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 5.78e-05 (Fisher's exact test), Q value = 0.028

Table S37.  Gene #27: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
16Q GAIN CNV 3 8 13 14
16Q GAIN WILD-TYPE 21 4 4 9

Figure S37.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.67e-06 (Fisher's exact test), Q value = 0.00087

Table S38.  Gene #27: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
16Q GAIN CNV 2 19 17
16Q GAIN WILD-TYPE 21 13 4

Figure S38.  Get High-res Image Gene #27: '16q gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 8.31e-05 (Fisher's exact test), Q value = 0.04

Table S39.  Gene #28: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
19P GAIN CNV 9 10 18 5
19P GAIN WILD-TYPE 20 9 1 5

Figure S39.  Get High-res Image Gene #28: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000204 (Fisher's exact test), Q value = 0.099

Table S40.  Gene #28: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
19P GAIN CNV 10 12 19
19P GAIN WILD-TYPE 13 20 2

Figure S40.  Get High-res Image Gene #28: '19p gain' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 2.32e-05 (Fisher's exact test), Q value = 0.012

Table S41.  Gene #29: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
19Q GAIN CNV 8 10 18 4
19Q GAIN WILD-TYPE 21 9 1 6

Figure S41.  Get High-res Image Gene #29: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 2.87e-06 (Fisher's exact test), Q value = 0.0015

Table S42.  Gene #30: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
20P GAIN CNV 4 16 12 6
20P GAIN WILD-TYPE 25 3 7 4

Figure S42.  Get High-res Image Gene #30: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 2.57e-05 (Fisher's exact test), Q value = 0.013

Table S43.  Gene #30: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
20P GAIN CNV 3 8 8 18
20P GAIN WILD-TYPE 21 4 9 5

Figure S43.  Get High-res Image Gene #30: '20p gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1.7e-06 (Fisher's exact test), Q value = 0.00088

Table S44.  Gene #31: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
20Q GAIN CNV 5 17 13 6
20Q GAIN WILD-TYPE 24 2 6 4

Figure S44.  Get High-res Image Gene #31: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.0097

Table S45.  Gene #31: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
20Q GAIN CNV 4 10 8 18
20Q GAIN WILD-TYPE 20 2 9 5

Figure S45.  Get High-res Image Gene #31: '20q gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'Xq gain' versus 'CN_CNMF'

P value = 0.000212 (Fisher's exact test), Q value = 0.1

Table S46.  Gene #33: 'Xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 29 19 19 10
XQ GAIN CNV 1 8 10 2
XQ GAIN WILD-TYPE 28 11 9 8

Figure S46.  Get High-res Image Gene #33: 'Xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'Xq gain' versus 'MRNASEQ_CNMF'

P value = 5.7e-07 (Fisher's exact test), Q value = 3e-04

Table S47.  Gene #33: 'Xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
XQ GAIN CNV 0 10 6 5
XQ GAIN WILD-TYPE 24 2 11 18

Figure S47.  Get High-res Image Gene #33: 'Xq gain' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 6.94e-05 (Fisher's exact test), Q value = 0.034

Table S48.  Gene #49: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
9P LOSS CNV 10 0 1 0
9P LOSS WILD-TYPE 14 12 16 23

Figure S48.  Get High-res Image Gene #49: '9p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7.88e-06 (Fisher's exact test), Q value = 0.004

Table S49.  Gene #49: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 23 32 21
9P LOSS CNV 10 0 1
9P LOSS WILD-TYPE 13 32 20

Figure S49.  Get High-res Image Gene #49: '9p loss' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.000211 (Fisher's exact test), Q value = 0.1

Table S50.  Gene #61: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 24 12 17 23
17P LOSS CNV 12 0 5 1
17P LOSS WILD-TYPE 12 12 12 22

Figure S50.  Get High-res Image Gene #61: '17p loss' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Molecular subtypes file = ACC-TP.transferedmergedcluster.txt

  • Number of patients = 77

  • Number of significantly arm-level cnvs = 68

  • Number of molecular subtypes = 8

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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